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comparison test-data/command-epifinder.txt @ 0:ef26009cd70a draft

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Uploaded version 1.1
author bioinformatics_lab_ufsc
date Thu, 25 Nov 2021 01:26:36 +0000
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1
2 ---- Running Parameters ----
3 BepiPred-2.0 Threshold : 0.6
4 Min epitope length : 10
5 Max epitope length : 30
6
7 ---- Softwares Threshold ----
8 Emini : 0.8
9 Parker : 0.8
10 Chou Fosman : 0.8
11 Karplus Schulz : 0.8
12 Kolaskar : 0.8
13
14 ---- Proteomes ----
15 Alias File
16 test_proteom /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta
17
18 ---- Blast ----
19 Identity : 90.0
20 Cover : 90.0
21 Word size : 4
22 Task blastp-short: blastp-short
23
24 ---- Stats ----
25 Processed proteins : 6
26 NGlycosylated proteins : 0
27 Identified epitopes : 3
28 N-glycosylated epitopes: 0
29
30 ---- Protein Summary ----
31 Id Epitopes N-Glyc
32 5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta 0 0
33 4XAK_A Chain A of Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD 0 0
34 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation 1 0
35 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 0
36 5C0N_A Chain A of Development of a therapeutic monoclonal antibody that targets secreted fatty acid-binding protein aP2 to treat type 2 diabetes. 0 0
37 4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2 0 0
38
39 ---- Epitopes list ----
40 N Id Epitope Start End N-Glyc N-Glyc-Count N-Glyc-Motifs Length MW(kDa) I.P Hydropathy All Matches Cover Avg Cover BepiPred2 Emini Parker Chou Fosman Karplus Schulz Kolaskar test_proteom_count test_proteom_acc test_proteom_count test_proteom_id
41 1 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation PETQSSHSAW 73 83 N 0 - 10 1.13 5.25 -1.40 0.90 0.98 0.65 2.57 4.19 1.13 1.04 0.99 1 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 1 4WFF_B(100.00,100.00)
42 2 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation AIFLKWHVPPELVR 149 163 N 0 - 14 1.71 8.80 0.42 0.07 0.60 0.64 0.82 -1.83 0.83 0.96 1.10 2 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 4WFF_B(100.00,100.00),4WFF_A(100.00,100.00)
43 3 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation LKWHVPPELVRVLSA 150 165 N 0 - 15 1.74 8.75 0.39 0.07 0.59 0.63 0.81 -1.70 0.84 0.96 1.11 2 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 4WFF_B(100.00,100.00),4WFF_A(100.00,100.00)
44
45 ---- Epitopes topology ----
46 N Id Method Threshold Avg Score Cover Epitope Start End N-Glyc N-Glyc-Count N-Glyc-Motifs Length kDa I.P Avg Hydropathy Avg Cover
47 1 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation BepiPred-2.0 0.60 0.65 - PETQSSHSAW 73 83 N 0 - 10 1.13 5.25 -1.40 0.98
48 Emini 0.80 2.57 0.90 EEEEEEEEE.
49 Parker 0.80 4.19 1.00 EEEEEEEEEE
50 Chou Fosman 0.80 1.13 1.00 EEEEEEEEEE
51 Karplus Schulz 0.80 1.04 1.00 EEEEEEEEEE
52 Kolaskar 0.80 0.99 1.00 EEEEEEEEEE
53 All matches - - 0.90 EEEEEEEEE.
54 N-Glyc - - - ..........
55 Hydropathy - -1.40 - --------+-
56 2 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation BepiPred-2.0 0.60 0.64 - AIFLKWHVPPELVR 149 163 N 0 - 14 1.71 8.80 0.42 0.60
57 Emini 0.80 0.82 0.43 .....EEEE.EE..
58 Parker 0.80 -1.83 0.07 .......E......
59 Chou Fosman 0.80 0.83 0.50 .....EEEEEEE..
60 Karplus Schulz 0.80 0.96 1.00 EEEEEEEEEEEEEE
61 Kolaskar 0.80 1.10 1.00 EEEEEEEEEEEEEE
62 All matches - - 0.07 .......E......
63 N-Glyc - - - ..............
64 Hydropathy - 0.42 - ++++---+---++-
65 3 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation BepiPred-2.0 0.60 0.63 - LKWHVPPELVRVLSA 150 165 N 0 - 15 1.74 8.75 0.39 0.59
66 Emini 0.80 0.81 0.40 ..EEEE.EE......
67 Parker 0.80 -1.70 0.07 ....E..........
68 Chou Fosman 0.80 0.84 0.47 ..EEEEEEE......
69 Karplus Schulz 0.80 0.96 1.00 EEEEEEEEEEEEEEE
70 Kolaskar 0.80 1.11 1.00 EEEEEEEEEEEEEEE
71 All matches - - 0.07 ....E..........
72 N-Glyc - - - ...............
73 Hydropathy - 0.39 - +---+---++-++-+
74 Generated files:
75 ./command-epifinder-parameters.txt
76 ./command-epifinder-protein-summary.tsv
77 ./command-epifinder-topology.tsv
78 ./command-epifinder-epitope-detail.tsv
79 ./command-epifinder-scores.tsv
80 ./command-epifinder-epitopes-fasta.fasta